I have a smart campaign running with a list of email domains that should be blacklisted. If I go into a contact (who's domain is black listed), and deselect them as being blacklisted, does this process overwrite the work of the live smart campaign? The qualification rules in my smart list state that a lead can run through the flow 'every time'. Does this mean at some point it will be switched back to being blacklisted? Perhaps after the record has been updated?

Doesn't directly answer your question, but if you're looking to globally blacklist certain users, it probably makes sense to use a segmentation, such as a Email Status Segmentation or Lifecycle Status Segmentation.